Engineers and Architects: Shelter Construction by Male Visayan Warty Pigs (Sus cebifrons negrinus) in Negros Island, Philippines

It is largely unknown how mammalian genomes evolve under rapid speciation and environmental adaptation. An excellent model for understanding fast evolution is provided by the genus Sus, which diverged relatively recently and lacks postzygotic isolation. Here, we present a high-quality reference genome of the Visayan warty pig, which is specialized to a tropical island environment. Comparing the genome sequences and chromatin contact maps of the Visayan warty pig (Sus cebifrons) and domestic pig (Sus scrofa), we characterized the dynamics of chromosomal structure evolution during Sus speciation, revealing the similar chromosome conformation as the potential biological mechanism of frequent postdivergence hybridization among Suidae. We further investigated the different signatures of adaptive selection and domestication in Visayan warty pig and domestic pig with specific emphasize on the evolution of olfactory and gustatory genes, elucidating higher olfactory diversity in Visayan warty pig and positive and relaxed evolution of bitter and fat taste receptors, respectively, in domestic pig. Our comprehensive evolutionary and comparative genome analyses provide insight into the dynamics of genomes and how these change over relative short evolutionary times, as well as how these genomic differences encode for differences in the phenotypes.

Chapter 8 - Suidae and Tayassuidae

Retrospective characterization of reproductive tract lesions in relation to age, parity, and contraception in captive suidae and tayassuidae

Many species have gone extinct as a result of human neglect and various environmental influences. Monitoring these species has proven to be a challenge due to their small population, remote habitats, and evasiveness, among other reasons. Nonetheless, they can be routinely tracked by using CCTV cameras. This project made use of a transfer learning approach to detect the presence of Malayan civets (Viverra tangalunga), Visayan leopard cats (Prionailurus javanensis sumatranus), Visayan spotted deer (Rusa alfredi) and Visayan warty pigs (Sus cebifrons) in the forests of Negros Island. We also developed a web application to record camera data and assign timestamps. The setup consisted of a Raspberry Pi 3B+ and a Raspberry Pi camera module powered by a solar power bank. The method used YOLOv5n, a lightweight object detection algorithm, to detect the four species. The trained model yielded 91% mAP, 64% mAP@0.5:0.95, and the following average precisions: 94% (Visayan warty pig), 91% (Malayan civet), 88% (Visayan leopard cat), and 91% (Visayan spotted deer) with 4.5 GFLOPs.

Genome Sequencing of the Endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) Reveals Potential Mechanisms of Evolutionary Specialization.

Among the artiodactyla, the suids are a group whose digestive physiology has hardly been investigated. The apparent digestibilities (aD) of macronutrients were measured in captive specimens of warthog (Phacochoerus africanus), red river hog (Potamochoerus porcus), and Visayan warty pigs (Sus cebifrons), and compared with those reported for babirusa (Babyrousa babyrussa) from the same facility on a similar diet. The animals were fed mixed diets of pelleted feed, grains, fruits, and vegetables; dietary neutral detergent fiber (NDF) ranged from 17 to 26% dry matter. aD of organic matter and protein ranged from 72 to 89 and 70 to 82%, respectively. Although red river hogs and warty pigs achieved aD of NDF of 41-54%, this value was higher both in warthogs (63-66%) and babirusa (61-63%). aD of acid detergent fiber was comparatively low in red river hogs (4%), warty pigs (22%), and babirusa (13-25%) but high in warthog (59-62%). Comparison with additional literature data (including peccaries) indicates that in spite of differences in digestive anatomy, suids and peccaries are similar, and resemble other herbivores in fundamental characteristics, such as the negative influence of fiber on overall digestibility, or the positive influence of dietary protein on protein digestion. Although the existing data are equivocal as to a superior fiber digestion in peccaries as compared with other wild suids, the results suggest that warthogs are more efficient than other wild suids or peccaries in terms of fiber digestion. Zoo Biol 27:305-319, 2008. (c) 2008 Wiley-Liss, Inc.

The author conducted a survey in 1985 that revealed dismal prospects for two endangered Philippine mammals. Habitat destruction and hunting pressure have caused local extinction of the spotted deer and the warty pig in the Visayan Islands, and the remaining populations are not expected to survive very much longer if current practices continue. The country's Bureau of Forest Development wants to establish a sanctuary for the deer and has started a captive breeding project, but the depressed state of the economy and political unrest make their work extremely difficult.

BackgroundThe integration of nuclear mitochondrial DNA (mtDNA) into the mammalian genomes is an ongoing, yet rare evolutionary process that produces nuclear sequences of mitochondrial origin (NUMT). In this study, we identified and analysed NUMT inserted into the pig (Sus scrofa) genome and in the genomes of a few other Suinae species. First, we constructed a comparative distribution map of NUMT in the Sscrofa11.1 reference genome and in 22 other assembled S. scrofa genomes (from Asian and European pig breeds and populations), as well as the assembled genomes of the Visayan warty pig (Sus cebifrons) and warthog (Phacochoerus africanus). We then analysed a total of 485 whole genome sequencing datasets, from different breeds, populations, or Sus species, to discover polymorphic NUMT (inserted/deleted in the pig genome). The insertion age was inferred based on the presence or absence of orthologous NUMT in the genomes of different species, taking into account their evolutionary divergence. Additionally, the age of the NUMT was calculated based on sequence degradation compared to the authentic mtDNA sequence. We also validated a selected set of representative NUMT via PCR amplification.ResultsWe have constructed an atlas of 418 NUMT regions, 70 of which were not present in any assembled genomes. We identified ancient NUMT regions (older than 55 million years ago, Mya) and NUMT that appeared at different time points along the Suinae evolutionary lineage. We identified very recent polymorphic NUMT (private to S. scrofa, with < 1 Mya), and more ancient polymorphic NUMT (3.5–10 Mya) present in various Sus species. These latest polymorphic NUMT regions, which segregate in European and Asian pig breeds and populations, are likely the results of interspecies admixture within the Sus genus.ConclusionsThis study provided a first comprehensive analysis of NUMT present in the Sus scrofa genome, comparing them to NUMT found in other species within the order Cetartiodactyla. The NUMT-based evolutionary window that we reconstructed from NUMT integration ages could be useful to better understand the micro-evolutionary events that shaped the modern pig genome and enriched the genetic diversity of this species.

Restraint is thought to be essential to enable the reciprocity needed for play fighting to remain playful. Descriptions of playing in pigs suggest that they do not exhibit restraint. Analysis of videotaped sequences of play fighting in captive family groups of warty pigs was used to test three hypotheses about restraint and reciprocity. Hypothesis 1 asserts that the lack of restraint arises from neither participant handicapping its actions in favour of its opponent: this was supported. Hypothesis 2 asserts that the winner of a contest will show restraint by not prosecuting further attack: this was not supported. However, the winner did refrain from attacking if the loser signalled submission. Hypothesis 3 asserts that restraint by the winner will allow reciprocal attacks by the loser — this was supported. The dissociation of restraint and reciprocity evident in the pigs offers some new insights into the evolution of play fighting.

Rattlesnake envenomation is an important cause of morbidity and mortality in humans and animals in the southwestern United States and elsewhere. Two Visayan warty pigs (Sus cebifrons) from a regional zoo were submitted for autopsy after being found dead close to a southern Pacific rattlesnake (Crotalus helleri) in their enclosure. Both pigs had severe regionally extensive cutaneous, subcutaneous, and muscle hemorrhage and edema with myonecrosis. Additionally, both pigs had lesions consistent with puncture wounds within the oral cavity, and one pig had a similar wound on a forelimb. The history, and gross and histologic findings, were consistent with envenomation by rattlesnake bite. There are few documented cases of snakebite envenomation in pigs, and it had been suggested that pigs may have some degree of resistance to envenomation. Our results indicate that warty pigs are susceptible to the action of rattlesnake venom.

Animal Behavior Not too long ago, it was argued that using tools was a hallmark of being human. However, this argument has been dispelled by more recent behavioral studies on other species—first by observations in great apes, then in species more distantly related to humans, such as crows and dolphins. Root-Bernstein et al. have discovered that the Visayan warty pig can use tools too. Female pigs of this critically endangered species from the Philippines use sticks and bark as digging tools during nest construction. The first observations were made opportunistically and then additional occurrences of the behavior were noticed after the motivation for digging was realized. Although these few observations were made on captive animals, they emphasize that we still have much to learn about the other animals that inhabit this planet even as they approach extinction. Mamm. Biol. 98 , 102 (2019).

The list of threatened and endangered species is growing rapidly, due to various anthropogenic causes. Many endangered species are present in captivity and actively managed in breeding programs in which often little is known about the founder individuals. Recent developments in genetic research techniques have made it possible to sequence and study whole genomes. In this study we used the critically endangered Visayan warty pig (Sus cebifrons) as a case study to test the use of genomic information as a tool in conservation management. Two captive populations of S. cebifrons exist, which originated from two different Philippine islands. We found some evidence for a recent split between the two island populations; however all individuals that were sequenced show a similar demographic history. Evidence for both past and recent inbreeding indicated that the founders were at least to some extent related. Together with this, the low level of nucleotide diversity compared to other Sus species potentially poses a threat to the viability of the captive populations. In conclusion, genomic techniques answered some important questions about this critically endangered mammal and can be a valuable toolset to inform future conservation management in other species as well.

Cooperation improves the access of wild boars (Sus scrofa) to food sources

The wild boar (Sus scrofa Linnaeus, 1758) as secondary reservoir of Fasciola hepatica in Galicia (NW Spain)

An outbreak of Salmonella enterica serotype Choleraesuis enteritis occurred in two juvenile goitered gazelles and an adult Malayan tapir over a period of 5 wk at the Minnesota Zoo. Diagnosis was made postmortem on one gazelle and one tapir, and a second gazelle was diagnosed via fecal culture. The death of the tapir was attributed to S. enterica serovar Choleraesuis septicemia, while salmonellosis was considered to be a contributing factor besides ostertagiasis for the death of one goitered gazelle and for the diarrhea of another goitered gazelle. A third gazelle became ill in the same time period, but Salmonella infection was not confirmed by culture. All exhibited the clinical signs of profuse, watery diarrhea. The gazelles developed a protein-losing enteropathy, and the tapir showed signs of sepsis and endotoxemia. Serotyping and pulsed-field gel electrophoresis revealed the Salmonella isolates to be indistinguishable from each other. One year prior to this outbreak, Salmonella sp. was cultured from a Visayan warty pig (Sus cebifrons) housed in the same building as the tapir. After further investigation into the outbreak, spread of this pathogen was speculated to be associated with human movement across animal areas.